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29 Open 239 Closed
29 Open 239 Closed
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Issues list

feat(Summary workflow): additional annotation dependent metrics enhancement New feature or request low priority Not important at the moment
#468 opened Aug 18, 2023 by ninsch3000
chore: migrate containers from dockerhub.io/apaeval to biocontainers
#467 opened Aug 17, 2023 by ninsch3000
feat(Summary workflow): check that PAS are reported as single nucleotide in input bed enhancement New feature or request
#458 opened Jan 10, 2023 by ninsch3000
feat(Execution workflows / Utils): making RefSeq annotations work for QAPA and PAQR. blocked Something prevents progress enhancement New feature or request
#457 opened Dec 20, 2022 by mrgazzara
3
chore: remove unnecessary requirement in identification swf low priority Not important at the moment
#456 opened Nov 29, 2022 by dominikburri
refactor: Singularity from conda environment might cause errors low priority Not important at the moment
#418 opened Sep 7, 2022 by dominikburri
1
feat(Execution workflow): LABRAT feature to reuse previous makeTFfasta output enhancement New feature or request low priority Not important at the moment
#406 opened Aug 9, 2022 by mrgazzara
2
fix(Summary workflows): don't overwrite previous results on new run bug Something isn't working low priority Not important at the moment nextflow
#400 opened Aug 5, 2022 by ninsch3000
2
docs(Summary Workflows): Logging documentation Improvements or additions to documentation good first issue Good for newcomers low priority Not important at the moment
#394 opened Jul 28, 2022 by ninsch3000
4 tasks
feat(Execution workflow): CSI-UTR - report Format 04 BED file in workflow (per-PAS fractional relative usage)
#388 opened Jul 18, 2022 by SamBryce-Smith
@yuukiiwa
4
docs(Execution workflow): update output file specifications for reporting region-level 'polyA site usage scores' documentation Improvements or additions to documentation
#380 opened Jul 13, 2022 by SamBryce-Smith
2 tasks
@SamBryce-Smith
feat(Summary workflows): new SWF for relative usage quantification meta Meta issue (spawns or lists dependent issues)
#371 opened Jul 7, 2022 by ninsch3000
4 tasks
chore(CommBench): Meta issue manuscripts meta Meta issue (spawns or lists dependent issues)
#335 opened Jul 6, 2022 by uniqueg Community benchmarking manuscript
feat(Summary workflow): Utils script/module to filter and convert ground truth TPM data to be compatible with relative quantification benchmark high priority
#301 opened Jun 12, 2022 by faricazjj
1
@yuukiiwa @SamBryce-Smith @mrgazzara
3
feat(Summary workflows): Differential summary workflow low priority Not important at the moment
#294 opened Jun 12, 2022 by faricazjj
1
feat(Publication): Plot outside of OpenEBench duplicate This issue or pull request already exists
#290 opened Jun 12, 2022 by faricazjj
2
feat(Execution workflow):Time and memory usage
#270 opened Jun 12, 2022 by faricazjj
@mrgazzara @pjewell-biociphers
1
fix(Execution workflow): APAtrap input parameter boolean check bug Something isn't working
#244 opened May 6, 2022 by faricazjj
@faricazjj
refactor: update Snakemake version in apaeval_env.yaml enhancement New feature or request low priority Not important at the moment
#223 opened Apr 1, 2022 by ninsch3000
feat(Utils): BAM to FASTQ
#209 opened Jan 11, 2022 by dominikburri
@mrgazzara
3
docs: prefer relative paths if possible documentation Improvements or additions to documentation good first issue Good for newcomers low priority Not important at the moment
#192 opened Nov 10, 2021 by dominikburri
feat(Utils): add tool to convert reference PAS bed to gtf enhancement New feature or request
#190 opened Nov 10, 2021 by ninsch3000
feat(Utils): Add utilility to sort a BED file by chromosome and coordinate
#186 opened Oct 13, 2021 by SamBryce-Smith
1
@grexor
test: Add genome fasta file to test_data directory
#178 opened Sep 23, 2021 by SamBryce-Smith
@SamBryce-Smith @mrgazzara
docs: update participant contributions documentation Improvements or additions to documentation question Further information is requested
#111 opened Jun 3, 2021 by FitzsimmonsCM
@FitzsimmonsCM @ninsch3000 @chelseaherdman
72
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